Reputation mechanics

[Kobal2fr]

Nothing's broken.

Reputation is based on three things.

1) global standing

Each turn you spend allied with one faction gives you +0.01 rep points, while each turn you spend at war with someone gives you -0.03. Also, reputation is normalized towards Mixed every turn. Since you're at war with the rebels by default, you need to have at least 3 allies at all times just to maintain your reputation, and 4 to slooooowly climb the ladder.
Unsavory thing : the factions you destroy are still technically at war with you, even if they don't exist anymore. The only way to avoid this is to make peace with them when they're down to their last province and let them die to rebels and/or another faction.

2) general behavior

helping an ally in battle gives you good points.
Breaking alliances either through diplomacy or outright betrayal, cancelling trade rights or mil rights, sending armies through allied lands without asking for mil rights first, breaking ceasefires (a ceasefire guarantees 4 turns of peace, after that it's fair game), all of this will give you bad points in huge amounts.
I believe captured assassination attempts and spies also make you untrustworthy, and even more so if you tried to kill a royal.

3) behavior in battle
liberating prisonners makes you trustworthy, ransoming gives you a few bad points, killing them a lot.
Same goes for cities : occupy gives you good points, sacking gives a few bad points, genocide tanks your rep.

BTW, all the things that give "good points" give them in trace amounts, while pretty much everything you do wrong earns you a big fat load of mistrust.

I may have forgotten some stuff, but them's the breaks : don't be an ass, be allied with as many factions as you can at all times, make one war at a time.

EDIT : oh, and getting back to your specific case, well there's your problem : you have two wars in progress (and they still are even if you destroyed the offending factions), and no allies. So your rep goes down overtime.